DNA is a complex macromolecule whose immunological activities are influenced by its base composition and base modification, as well as helical orientation. Certain unusual DNA structures (e.g., Z-DNA) can induce significant antibody responses when administered to normal mice. In addition, bacterial DNA, as well as certain synthetic unmethylated CpG sequences can induce proliferation and immunoglobulin (Ig) production by murine B cells. Unmethylated CpG dinucleotides are more frequent in the genomes of bacteria and viruses than vertebrates. Recent studies suggest that immune recognition of these motifs may contribute to the host's innate immune response. D. M. Klinman et al., “CpG Motifs Present in Bacterial DNA Rapidly Induce Lymphocytes to Secrete Interleukin 6, Interleukin 12, and Interferon γ,” 93 Proc. Natl. Acad. Sci. USA 2879 (1996); A.-K. Yi et al., “Rapid Immune Activation by CpG Motifs in Bacterial DNA,” 157 J. Immun. 5394 (1996); Hua Liang et al., “Activation of Human B Cells by Phosphorothioate Oligodeoxynucleotides,” 98 J. Clin. Invest. 1119 (1996); A. M. Krieg et al., “CpG Motifs in Bacterial DNA Trigger Direct B-Cell Activation,” 374 Nature 546 (1995).
In mice, CpG DNA induces proliferation in almost all (>95%) of B cells and increases Ig secretion. This B cell activation by CpG DNA is T cell independent and antigen non-specific. In addition to its direct effects on B cells, CpG DNA also directly activates monocytes, macrophages, and dendritic cells to secrete a variety of cytokines. These cytokines stimulate natural killer (NK) cells to secrete γ-inteferon (IFN-γ) and have increased lytic activity. Examples of which can be found in International Patent Applications WO 95/26204, WO 96/02555, WO 98/11211, WO 98/18810, WO 98/37919, WO 98/40100, WO 98/52581, and PCT/US98/047703; U.S. patent applications Ser. Nos. 08/738,652 and 09/136,138; and U.S. Pat. No. 5,663,153.
Although bacterial DNA and certain CpG sequences can induce responses from human cells (Ballas et al., “Induction of NK Activity in Murine and Human Cells by CpG Motifs in Oligodeoxynucleotides and Bacterial DNA,” 157 J. Immunol. 1840 (1996)), individual subjects show considerable heterogeneity in their response to different CpG sequences. As disclosed herein, CpG sequences that strongly stimulate cells from some subjects are virtually inactive on cells from other subjects. These different responses can make it difficult to induce a therapeutic immune response in all members of a diverse population using a single CpG sequence, even if such a sequence is expressed repetitively in a given oligodeoxynucleotide. Thus, there exists a need to identify different CpG sequences that together are capable of optimally inducing an immune response in cells from all members of a target population.